java.lang.Object
- gov.nih.mipav.model.file.FileBase
- - gov.nih.mipav.model.file.FilePARREC

```
public class FilePARREC
extends FileBase
```
The class reads and writes PAR/REC files. A right handed coordinate system is used with the positive axis pointing (Anterior/Posterior)A->P, (Foot/Head)F->H, and (Right/Left)R->L. * Updated September 16, 2011 by Beth Tyrie // This explains the derivation of the dicom transformation matrix and origin from the PARREC parameters. // The axial PAR file is KKZ_130213_4_1.PAR // The first slice of the axial dicom file is 20131023203338769.MR.dcm // The sagittal PAR file is KKZ_130213_3_1.PAR // The first slice of the sagittal dicom file is 20131107105801812.MR.dcm. // The coronal PAR file is KKZ_130213_10_1.PAR // The first slice of the coronal dicom file is 20131107105805315.MR.dcm. // The angles are the same for the header volume parameters and for every slice int ori; final int axial = 1; final int sagittal = 2; final int coronal = 3; ori = coronal; double angulation_rl = 0.0; double angulation_ap = 0.0; double angulation_fh = 0.0; switch(ori) { case axial: angulation_rl = -8.700; angulation_ap = -4.865; angulation_fh = 3.364; break; case sagittal: angulation_rl = 0.305; angulation_ap = -4.280; angulation_fh = 4.083; break; case coronal: angulation_rl = 3.931; angulation_ap = -4.031; angulation_fh = 4.346; } double angX = 0.0; double angY = 0.0; double angZ = 0.0; switch(ori) { case axial: angX = angulation_rl; angY = angulation_ap; angZ = angulation_fh; break; case sagittal: angX = angulation_ap; angY = -angulation_fh; angZ = -angulation_rl; break; case coronal: angX = angulation_rl; angY = -angulation_fh; angZ = angulation_ap; } double Sx = Math.sin(angX * Math.PI/180.0); double Sy = Math.sin(angY * Math.PI/180.0); double Sz = Math.sin(angZ * Math.PI/180.0); double Cx = Math.cos(angX * Math.PI/180.0); double Cy = Math.cos(angY * Math.PI/180.0); double Cz = Math.cos(angZ * Math.PI/180.0); // EulerOrder = ORDER_XYZ; // This is the Transformation matrix shown in the dicom header // The dicom transformation matrix or image.getMatrix() is the transpose of the matrix given by getPatientOrientation(). // image.getMatrix() and getPatientOrientation() contain just the rotation component. double m00=Cy*Cz; double m01=-Cy*Sz; double m02=Sy; double m10=Cz*Sx*Sy+Cx*Sz; double m11=Cx*Cz-Sx*Sy*Sz; double m12=-Cy*Sx; double m20=-Cx*Cz*Sy+Sx*Sz; double m21=Cz*Sx+Cx*Sy*Sz; double m22=Cx*Cy; TransMatrix tr = new TransMatrix(4); switch (ori) { case axial: tr.M00 = (float)m00; tr.M01 = (float)m01; tr.M02 = (float)m02; tr.M03 = 0; tr.M10 = (float)m10; tr.M11 = (float)m11; tr.M12 = (float)m12; tr.M13 = 0; tr.M20 = (float)m20; tr.M21 = (float)m21; tr.M22 = (float)m22; tr.M23 = 0; tr.M30 = 0; tr.M31 = 0; tr.M32 = 0; tr.M33 = 1; break; case sagittal: tr.M00 = -(float)m20; tr.M01 = -(float)m21; tr.M02 = -(float)m22; tr.M03 = 0; tr.M10 = (float)m00; tr.M11 = (float)m01; tr.M12 = (float)m02; tr.M13 = 0; tr.M20 = -(float)m10; tr.M21 = -(float)m11; tr.M22 = -(float)m12; tr.M23 = 0; tr.M30 = 0; tr.M31 = 0; tr.M32 = 0; tr.M33 = 1; break; case coronal: tr.M00 = (float)m00; tr.M01 = (float)m01; tr.M02 = (float)m02; tr.M03 = 0; tr.M10 = (float)m20; tr.M11 = (float)m21; tr.M12 = (float)m22; tr.M13 = 0; tr.M20 = -(float)m10; tr.M21 = -(float)m11; tr.M22 = -(float)m12; tr.M23 = 0; tr.M30 = 0; tr.M31 = 0; tr.M32 = 0; tr.M33 = 1; } System.out.println("image transMatrix = " + tr); double resX = 0.0; double resY = 0.0; double resZ = 0.0; switch(ori) { case axial: resX = 0.859375; resY = 0.859375; resZ = 1.0; break; case sagittal: resX = 0.42857143; resY = 0.42857143; resZ = 5.0; break; case coronal: resX = 0.3515625; resY = 0.3515625; resZ = 3.3; } // The header volume offsets and the individual slice offsets are all different // The header volume offsets correspond to (xDim - 1)/2, (yDim - 1)/2, (zDim - 1)/2 // The slice offsets correspond to (xDim - 1)/2, (yDim - 1)/2, zSlice. double rl_offset_center = 0.0; double ap_offset_center = 0.0; double fh_offset_center = 0.0; switch(ori) { case axial: rl_offset_center = 6.655; ap_offset_center = 3.537; fh_offset_center = 22.171; break; case sagittal: rl_offset_center = 8.844; ap_offset_center = -3.225; fh_offset_center = -0.535; break; case coronal: rl_offset_center = 6.147; ap_offset_center = 16.846; fh_offset_center = 16.330; } double offsetX = 0.0; double offsetY = 0.0; double offsetZ = 0.0; switch(ori) { case axial: offsetX = rl_offset_center; offsetY = ap_offset_center; offsetZ = fh_offset_center; break; case sagittal: offsetX = ap_offset_center; offsetY = -fh_offset_center; offsetZ = -rl_offset_center; break; case coronal: offsetX = rl_offset_center; offsetY = -fh_offset_center; offsetZ = ap_offset_center; } double dimX = 0.0; double dimY = 0.0; double dimZ = 0.0; switch(ori) { case axial: dimX = 256; dimY = 256; dimZ = 140; break; case sagittal: dimX = 560; dimY = 560; dimZ = 31; case coronal: dimX = 512; dimY = 512; dimZ = 47; } double originX = offsetX - m00 * resX * (dimX-1)/2 - m01 * resY * (dimY-1)/2- m02 * resZ * (dimZ-1)/2; double originY = offsetY - m10 * resX * (dimX-1)/2 - m11 * resY * (dimY-1)/2 - m12 * resZ * (dimZ-1)/2; double originZ = offsetZ - m20 * resX * (dimX-1)/2 - m21 * resY * (dimY-1)/2 - m22 * resZ * (dimZ-1)/2; if (ori == sagittal) { originY = -originY; originZ = -originZ; } else if (ori == coronal) { originY = -originY; } // These are the origins shown for dicom slice 0 System.out.println("originX = " + originX); System.out.println("originY = " + originY); System.out.println("originZ = " + originZ);

Field Summary

Fields
Modifier and Type	Field	Description
`private int`	`bValueIndex`
`private int`	`bValuePos`	bFactorIndex
`private int[]`	`cardiacFrequency`
`private int`	`cardiacFrequencyIndex`
`private int`	`cardiacFrequencyPos`
`private int[]`	`cardiacPhaseNumber`
`private int`	`cardiacPhaseNumberIndex`
`private int`	`cardiacPhaseNumberPos`
`(package private) boolean`	`changeToUnsignedInts`
`private java.lang.String[]`	`contrastBolusAgent`
`private int`	`contrastBolusAgentIndex`
`private int`	`contrastBolusAgentPos`
`private java.lang.String[]`	`contrastBolusIngredient`
`private float[]`	`contrastBolusIngredientConcentration`
`private int`	`contrastBolusIngredientConcentrationIndex`
`private int`	`contrastBolusIngredientConcentrationPos`
`private int`	`contrastBolusIngredientIndex`
`private int`	`contrastBolusIngredientPos`
`private float[]`	`contrastBolusRoute`
`private int`	`contrastBolusRouteIndex`
`private int`	`contrastBolusRoutePos`
`private java.lang.String[]`	`contrastBolusStartTime`
`private int`	`contrastBolusStartTimeIndex`
`private int`	`contrastBolusStartTimePos`
`private float[]`	`contrastBolusTotalDose`
`private int`	`contrastBolusTotalDoseIndex`
`private int`	`contrastBolusTotalDosePos`
`private java.lang.String[]`	`contrastBolusVolume`
`private int`	`contrastBolusVolumeIndex`
`private int`	`contrastBolusVolumePos`
`private java.lang.String[]`	`contrastType`
`private int`	`contrastTypeIndex`
`private int`	`contrastTypePos`
`private int`	`counter`	counter
`private float[][]`	`diffusion`
`private java.lang.String[]`	`diffusionAnisotropyType`
`private int`	`diffusionAnisotropyTypeIndex`
`private int`	`diffusionAnisotropyTypePos`
`private float[]`	`diffusionBFactor`
`private int[]`	`diffusionBValueNumber`
`private int`	`diffusionBValueNumberIndex`
`private int`	`diffusionBValueNumberPos`
`private DTIParameters`	`dtiparams`	Object to save DWI paramters to
`private float[]`	`dynamicScanBeginTime`
`private int`	`dynamicScanBeginTimeIndex`
`private int`	`dynamicScanBeginTimePos`
`private int[]`	`dynamicScanNumber`
`private int`	`dynamicScanNumberIndex`
`private int`	`dynamicScanNumberPos`
`private int[]`	`echoNumber`
`private int`	`echoNumberIndex`
`private int`	`echoNumberPos`
`private float[]`	`echoTime`
`private int`	`echoTimeIndex`
`private int`	`echoTimePos`
`private java.lang.String`	`examName`	exam name
`private java.lang.String`	`fileDir`	File directory of the image.
`private FileInfoPARREC`	`fileInfo`	Reference to the file info. for an Analyze header
`private FileInfoPARREC[]`	`fileInfoArray`
`private java.lang.String`	`fileName`	File name of the image.
`private float[]`	`flipAngle`
`private int`	`flipAngleIndex`
`private int`	`flipAnglePos`
`private int[]`	`fmriStatusIndication`
`private int`	`fmriStatusIndicationIndex`
`private int`	`fmriStatusIndicationPos`
`private java.lang.String`	`foldover`
`private int[]`	`gradientOrientationNumber`
`private int`	`gradientOrientationNumberIndex`
`private int`	`gradientOrientationNumberPos`
`private int`	`gradIndex`
`private int`	`gradPos`	bFactorIndex
`static java.lang.String[]`	`hdrEXTENSIONS`	The extensions of ANALYZE file.
`private ModelImage`	`image`	The image read in from the file.
`private float[][]`	`imageAngulation`
`private int`	`imageAngulationIndex`
`private int`	`imageAngulationPos`
`private float[][]`	`imageOffcentre`
`private int`	`imageOffcentreIndex`
`private int`	`imageOffcentrePos`
`private int[]`	`imageTypeEDES`
`private int`	`imageTypeEDESIndex`
`private int`	`imageTypeEDESPos`
`private int[]`	`imageTypeMR`
`private int`	`imageTypeMRIndex`
`private int`	`imageTypeMRPos`
`static java.lang.String[]`	`imgEXTENSIONS`
`private float[]`	`inversionDelay`
`private int`	`inversionDelayIndex`
`private int`	`inversionDelayPos`
`private boolean`	`isSortedByVolumes`	normal par/rec are sorted by volumes...sometime, they are not sorted like this...instead they are based on slices if that is true, then we need to change around the image dataarray to make it sorted by volumes
`private int[]`	`labelType`
`private int`	`labelTypeIndex`
`private int`	`labelTypePos`
`private int[]`	`maximumRRInterval`
`private int`	`maximumRRIntervalIndex`
`private int`	`maximumRRIntervalPos`
`private int[]`	`minimumRRInterval`
`private int`	`minimumRRIntervalIndex`
`private int`	`minimumRRIntervalPos`
`private int[]`	`numberOfAverages`
`private int`	`numberOfAveragesIndex`
`private int`	`numberOfAveragesPos`
`private int`	`numSlices`	num slices per volume
`private int`	`numVolumes`	num vols in 4d dataset
`private int`	`originalDataType`
`private FileInfoPARREC`	`outInfo`	file info
`private java.lang.String`	`patientName`
`private java.lang.String`	`patientPosition`	patient position
`private java.lang.String`	`protocolName`	protocol name
`private float[]`	`rescaleIntercept`	floating point value = raw value/scaleSlope + rescaleIntercept/(rescaleSlope*scaleSlope)
`private float[]`	`rescaleSlope`
`private boolean`	`sameSliceScalings`	True if the 3 values are the same for all slices
`private float[]`	`scaleSlope`
`private int[]`	`scanningSequence`
`private int`	`scanningSequenceIndex`
`private int`	`scanningSequencePos`
`private int[]`	`scanPercentage`
`private int`	`scanPercentageIndex`
`private int`	`scanPercentagePos`
`private java.util.HashMap<java.lang.String,java.lang.Integer>`	`SliceMap`	slice map
`private int`	`sliceOrientIndex`
`private int`	`sliceOrientPos`
`private java.util.Vector<java.lang.String>`	`SliceParameters`	slice parameters
`private java.util.Vector<java.lang.String>`	`Slices`	slices
`private float[]`	`triggerTime`
`private int`	`triggerTimeIndex`
`private int`	`triggerTimePos`
`private int[]`	`turboFactor`
`private int`	`turboFactorIndex`
`private int`	`turboFactorPos`
`private java.lang.String`	`version`	version
`private java.util.HashMap<java.lang.String,java.lang.String>`	`VolMap`	vol map
`private java.util.HashMap<java.lang.String,java.lang.String>`	`VolParameters`	vol parameters
`private float`	`vox_offset`	Voxel offset tag used to read in the image.
`private int[]`	`windowCenter`
`private int`	`windowCenterIndex`
`private int`	`windowCenterPos`
`private int[]`	`windowWidth`
`private int`	`windowWidthIndex`
`private int`	`windowWidthPos`

Fields inherited from class gov.nih.mipav.model.file.FileBase
BIG_ENDIAN, bitsPerPixel, fileNames, LITTLE_ENDIAN, pBarVisible, raFile, READ, READ_WRITE

Constructor Summary

Constructors
Constructor	Description
`FilePARREC(java.lang.String[] fileNames)`	Creates a new FileAnalyze object.
`FilePARREC(java.lang.String fName, java.lang.String fDir)`	Constructs new file object.
`FilePARREC(java.lang.String fileName, java.lang.String fileDirectory, FileInfoBase fileInfo)`	Constructor used by FileIO to write an image
`FilePARREC(java.lang.String fileName, java.lang.String fileDirectory, FileInfoPARREC[] fileInfoArray, boolean changeToUnsignedInts)`	Constructor used by FileIO to write an image

Method Summary

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`private java.util.HashMap<java.lang.String,java.lang.Integer>`	`buildParSliceMap()`
`private java.util.HashMap<java.lang.String,java.lang.String>`	`buildParVolMap()`
`static TransMatrix`	`ConvertToMIPAVConvention(TransMatrix mat)`	Converts translation matrix to mipav specific format
`ModelImage`	`createImage()`	DOCUMENT ME!
`void`	`finalize()`	Prepares this class for cleanup.
`static java.lang.String[]`	`getCompleteFileNameList(java.lang.String absolutePath)`	Returns the complete list of file names according to given file name.
`java.lang.String[]`	`getCompleteFileNameListDefault(java.lang.String absolutePath)`	Gets the header and image file names given a header or image file name
`FileInfoPARREC`	`getFileInfo()`	Returns the FileInfoAnalyze read from the file.
`java.lang.String`	`getHeaderFile()`
`static java.lang.String`	`getHeaderFile(java.lang.String[] fileNames)`	======= Returns the header file.
`java.lang.String[]`	`getImageFiles()`	Returns the image file list.
`static java.lang.String[]`	`getImageFiles(java.lang.String[] fileNames)`	Returns the image file list.
`private int`	`getOffset(FileInfoPARREC fileInfo)`	Helper method to calculate the offset for getting only the middle analyze image slice from the 3D file.
`static boolean`	`isHeaderFile(java.lang.String absolutePath)`	Return true if the file specified by absolutePath is header file of PARREC.
`static boolean`	`isImageFile(java.lang.String absolutePath)`	Return true if the file specified by absolutePath is image file of PARREC.
`static TransMatrix`	`makeRotationMatrix(int[] size, double[] rotations)`	Makes rotation matrix based on image angulations that were stored in header and converted to orientation-specific values.
`static TransMatrix`	`makeTranslationMatrix(double[] translations)`	Makes rotation matrix based on image off-centres that were stored in header and converted to orientation-specific values.
`boolean`	`readHeader(java.lang.String imageFileName, java.lang.String fileDir)`	Reads the analyze header and stores the information in fileInfo.
`ModelImage`	`readImage(boolean one)`	Reads an PAR/REC image file by reading the header then making a FileRaw to read the image for all filenames in the file list.
`void`	`readImage(float[] buffer)`	Reads in a PAR/REC image (first the header file, then the raw file)
`void`	`setImage(ModelImage image)`
`private void`	`updateStartLocations(FileInfoBase[] fileInfo)`	Updates the start locations.
`private void`	`updateTransformMatrix(FileInfoPARREC fileInfo, ModelImage image)`
`private void`	`updateUnitsOfMeasure(FileInfoPARREC fileInfo, ModelImage image)`	Updates the units of Measure in the file info based on the voxUnits from an Analyze Header.
`void`	`writeHeader(ModelImage writeImage, java.lang.String headerFileName, int beginSlice, int endSlice, int beginTime, int endTime, boolean rescale)`
`void`	`writeImage(ModelImage image, FileWriteOptions options)`	Writes a PAR/REC format image and header.

Methods inherited from class gov.nih.mipav.model.file.FileBase
addProgressChangeListener, bytesToDouble, bytesToFloat, bytesToInt, bytesToShort, doubleToBytes, fireProgressStateChanged, fireProgressStateChanged, fireProgressStateChanged, floatToBytes, getBufferDouble, getBufferFloat, getBufferInt, getBufferLong, getBufferShort, getBufferUShort, getDataType, getDouble, getFloat, getInt, getLong, getProgressChangeListeners, getRaFile, getSignedShort, getString, getUInt, getUnsignedByte, getUnsignedShort, intToBytes, isBigEndian, isProgressBarVisible, linkProgress, longToBytes, readDouble, readFloat, readInt, readLong, readShort, readString, readUnsignedShort, removeProgressChangeListener, setBigEndian, setBufferFloat, setBufferInt, setBufferLong, setBufferShort, setBufferString, setDataType, setEndianess, shortToBytes, writeBytes, writeDouble, writeFloat, writeInt, writeLong, writeShort

Methods inherited from class java.lang.Object
clone, equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

hdrEXTENSIONS

public static final java.lang.String[] hdrEXTENSIONS

The extensions of ANALYZE file.

imgEXTENSIONS

public static final java.lang.String[] imgEXTENSIONS

fileDir
```
private java.lang.String fileDir
```
File directory of the image.

fileInfo
```
private FileInfoPARREC fileInfo
```
Reference to the file info. for an Analyze header

fileName
```
private java.lang.String fileName
```
File name of the image.

image
```
private ModelImage image
```
The image read in from the file.

dtiparams
```
private DTIParameters dtiparams
```
Object to save DWI paramters to

vox_offset
```
private float vox_offset
```
Voxel offset tag used to read in the image.

fileInfoArray
```
private FileInfoPARREC[] fileInfoArray
```

outInfo
```
private FileInfoPARREC outInfo
```
file info

VolMap

private java.util.HashMap<java.lang.String,java.lang.String> VolMap

vol map

SliceMap

private java.util.HashMap<java.lang.String,java.lang.Integer> SliceMap

slice map

VolParameters

private java.util.HashMap<java.lang.String,java.lang.String> VolParameters

vol parameters

SliceParameters

private java.util.Vector<java.lang.String> SliceParameters

slice parameters

Slices

private java.util.Vector<java.lang.String> Slices

slices

version
```
private java.lang.String version
```
version

patientName
```
private java.lang.String patientName
```

examName
```
private java.lang.String examName
```
exam name

protocolName
```
private java.lang.String protocolName
```
protocol name

patientPosition

private java.lang.String patientPosition

patient position

foldover
```
private java.lang.String foldover
```

sliceOrientPos
```
private int sliceOrientPos
```

bValuePos
```
private int bValuePos
```
bFactorIndex

gradPos
```
private int gradPos
```
bFactorIndex

echoNumberPos
```
private int echoNumberPos
```

dynamicScanNumberPos
```
private int dynamicScanNumberPos
```

cardiacPhaseNumberPos
```
private int cardiacPhaseNumberPos
```

imageTypeMRPos
```
private int imageTypeMRPos
```

scanningSequencePos
```
private int scanningSequencePos
```

scanPercentagePos
```
private int scanPercentagePos
```

windowCenterPos
```
private int windowCenterPos
```

windowWidthPos
```
private int windowWidthPos
```

imageAngulationPos
```
private int imageAngulationPos
```

imageOffcentrePos
```
private int imageOffcentrePos
```

fmriStatusIndicationPos
```
private int fmriStatusIndicationPos
```

imageTypeEDESPos
```
private int imageTypeEDESPos
```

echoTimePos
```
private int echoTimePos
```

dynamicScanBeginTimePos
```
private int dynamicScanBeginTimePos
```

triggerTimePos
```
private int triggerTimePos
```

numberOfAveragesPos
```
private int numberOfAveragesPos
```

flipAnglePos
```
private int flipAnglePos
```

cardiacFrequencyPos
```
private int cardiacFrequencyPos
```

minimumRRIntervalPos
```
private int minimumRRIntervalPos
```

maximumRRIntervalPos
```
private int maximumRRIntervalPos
```

turboFactorPos
```
private int turboFactorPos
```

inversionDelayPos
```
private int inversionDelayPos
```

diffusionBValueNumberPos
```
private int diffusionBValueNumberPos
```

gradientOrientationNumberPos

private int gradientOrientationNumberPos

contrastTypePos
```
private int contrastTypePos
```

diffusionAnisotropyTypePos
```
private int diffusionAnisotropyTypePos
```

labelTypePos
```
private int labelTypePos
```

contrastBolusAgentPos
```
private int contrastBolusAgentPos
```

contrastBolusRoutePos
```
private int contrastBolusRoutePos
```

contrastBolusVolumePos
```
private int contrastBolusVolumePos
```

contrastBolusStartTimePos
```
private int contrastBolusStartTimePos
```

contrastBolusTotalDosePos
```
private int contrastBolusTotalDosePos
```

contrastBolusIngredientPos
```
private int contrastBolusIngredientPos
```

contrastBolusIngredientConcentrationPos

private int contrastBolusIngredientConcentrationPos

sliceOrientIndex
```
private int sliceOrientIndex
```

bValueIndex
```
private int bValueIndex
```

gradIndex
```
private int gradIndex
```

echoNumberIndex
```
private int echoNumberIndex
```

dynamicScanNumberIndex
```
private int dynamicScanNumberIndex
```

cardiacPhaseNumberIndex
```
private int cardiacPhaseNumberIndex
```

imageTypeMRIndex
```
private int imageTypeMRIndex
```

scanningSequenceIndex
```
private int scanningSequenceIndex
```

scanPercentageIndex
```
private int scanPercentageIndex
```

windowCenterIndex
```
private int windowCenterIndex
```

windowWidthIndex
```
private int windowWidthIndex
```

imageAngulationIndex
```
private int imageAngulationIndex
```

imageOffcentreIndex
```
private int imageOffcentreIndex
```

fmriStatusIndicationIndex
```
private int fmriStatusIndicationIndex
```

imageTypeEDESIndex
```
private int imageTypeEDESIndex
```

echoTimeIndex
```
private int echoTimeIndex
```

dynamicScanBeginTimeIndex
```
private int dynamicScanBeginTimeIndex
```

triggerTimeIndex
```
private int triggerTimeIndex
```

numberOfAveragesIndex
```
private int numberOfAveragesIndex
```

flipAngleIndex
```
private int flipAngleIndex
```

cardiacFrequencyIndex
```
private int cardiacFrequencyIndex
```

minimumRRIntervalIndex
```
private int minimumRRIntervalIndex
```

maximumRRIntervalIndex
```
private int maximumRRIntervalIndex
```

turboFactorIndex
```
private int turboFactorIndex
```

inversionDelayIndex
```
private int inversionDelayIndex
```

diffusionBValueNumberIndex
```
private int diffusionBValueNumberIndex
```

gradientOrientationNumberIndex

private int gradientOrientationNumberIndex

contrastTypeIndex
```
private int contrastTypeIndex
```

diffusionAnisotropyTypeIndex

private int diffusionAnisotropyTypeIndex

labelTypeIndex
```
private int labelTypeIndex
```

contrastBolusAgentIndex
```
private int contrastBolusAgentIndex
```

contrastBolusRouteIndex
```
private int contrastBolusRouteIndex
```

contrastBolusVolumeIndex
```
private int contrastBolusVolumeIndex
```

contrastBolusStartTimeIndex

private int contrastBolusStartTimeIndex

contrastBolusTotalDoseIndex

private int contrastBolusTotalDoseIndex

contrastBolusIngredientIndex

private int contrastBolusIngredientIndex

contrastBolusIngredientConcentrationIndex

private int contrastBolusIngredientConcentrationIndex

echoNumber
```
private int[] echoNumber
```

dynamicScanNumber
```
private int[] dynamicScanNumber
```

cardiacPhaseNumber
```
private int[] cardiacPhaseNumber
```

imageTypeMR
```
private int[] imageTypeMR
```

scanningSequence
```
private int[] scanningSequence
```

scanPercentage
```
private int[] scanPercentage
```

windowCenter
```
private int[] windowCenter
```

windowWidth
```
private int[] windowWidth
```

imageAngulation
```
private float[][] imageAngulation
```

imageOffcentre
```
private float[][] imageOffcentre
```

fmriStatusIndication
```
private int[] fmriStatusIndication
```

imageTypeEDES
```
private int[] imageTypeEDES
```

echoTime
```
private float[] echoTime
```

dynamicScanBeginTime
```
private float[] dynamicScanBeginTime
```

triggerTime
```
private float[] triggerTime
```

numberOfAverages
```
private int[] numberOfAverages
```

flipAngle
```
private float[] flipAngle
```

cardiacFrequency
```
private int[] cardiacFrequency
```

minimumRRInterval
```
private int[] minimumRRInterval
```

maximumRRInterval
```
private int[] maximumRRInterval
```

turboFactor
```
private int[] turboFactor
```

inversionDelay
```
private float[] inversionDelay
```

diffusionBFactor
```
private float[] diffusionBFactor
```

diffusionBValueNumber
```
private int[] diffusionBValueNumber
```

gradientOrientationNumber

private int[] gradientOrientationNumber

contrastType

private java.lang.String[] contrastType

diffusionAnisotropyType

private java.lang.String[] diffusionAnisotropyType

diffusion
```
private float[][] diffusion
```

labelType
```
private int[] labelType
```

contrastBolusAgent

private java.lang.String[] contrastBolusAgent

contrastBolusRoute
```
private float[] contrastBolusRoute
```

contrastBolusVolume

private java.lang.String[] contrastBolusVolume

contrastBolusStartTime

private java.lang.String[] contrastBolusStartTime

contrastBolusTotalDose
```
private float[] contrastBolusTotalDose
```

contrastBolusIngredient

private java.lang.String[] contrastBolusIngredient

contrastBolusIngredientConcentration

private float[] contrastBolusIngredientConcentration

counter
```
private int counter
```
counter

rescaleIntercept
```
private float[] rescaleIntercept
```
floating point value = raw value/scaleSlope + rescaleIntercept/(rescaleSlope*scaleSlope)

rescaleSlope
```
private float[] rescaleSlope
```

scaleSlope
```
private float[] scaleSlope
```

sameSliceScalings
```
private boolean sameSliceScalings
```
True if the 3 values are the same for all slices

originalDataType
```
private int originalDataType
```

isSortedByVolumes
```
private boolean isSortedByVolumes
```
normal par/rec are sorted by volumes...sometime, they are not sorted like this...instead they are based on slices if that is true, then we need to change around the image dataarray to make it sorted by volumes

numSlices
```
private int numSlices
```
num slices per volume

numVolumes
```
private int numVolumes
```
num vols in 4d dataset

changeToUnsignedInts
```
boolean changeToUnsignedInts
```

Constructor Detail

FilePARREC
```
public FilePARREC(java.lang.String[] fileNames)
```
Creates a new FileAnalyze object.

Parameters:

fileNames - DOCUMENT ME!

FilePARREC

public FilePARREC(java.lang.String fName,
                  java.lang.String fDir)

Constructs new file object.

Parameters:: fName - File name.; fDir - File directory.

FilePARREC

public FilePARREC(java.lang.String fileName,
                  java.lang.String fileDirectory,
                  FileInfoPARREC[] fileInfoArray,
                  boolean changeToUnsignedInts)

Constructor used by FileIO to write an image

Parameters:: fileName -; fileDirectory -; fileInfoPARREC - []; changeToUnsignedInts -

FilePARREC

public FilePARREC(java.lang.String fileName,
                  java.lang.String fileDirectory,
                  FileInfoBase fileInfo)

Constructor used by FileIO to write an image

Parameters:: fileName -; fileDirectory -; fileInfo -

Method Detail
- finalize
```
public void finalize()
```
  Prepares this class for cleanup. Calls the finalize method for existing elements, closes any open files and sets other elements to null.
  
  Overrides:
  
  finalize in class FileBase
- setImage
```
public void setImage(ModelImage image)
```
  Parameters:
  
  image -
- getCompleteFileNameList
```
public static java.lang.String[] getCompleteFileNameList(java.lang.String absolutePath)
```
  Returns the complete list of file names according to given file name.
  
  Parameters:
  
  absolutePath - one file name of PARREC.
  
  Returns:
  
  the complete list of file names.
- getHeaderFile
```
public static java.lang.String getHeaderFile(java.lang.String[] fileNames)
```
  ======= Returns the header file.
  
  Parameters:
  
  fileNames - DOCUMENT ME!
  
  Returns:
  
  DOCUMENT ME!
- getImageFiles
```
public static java.lang.String[] getImageFiles(java.lang.String[] fileNames)
```
  Returns the image file list.
  
  Parameters:
  
  fileNames - DOCUMENT ME!
  
  Returns:
  
  the image file list.
- isHeaderFile
```
public static boolean isHeaderFile(java.lang.String absolutePath)
```
  Return true if the file specified by absolutePath is header file of PARREC.
  
  Parameters:
  
  absolutePath - the file name including path information.
  
  Returns:
  
  true if the specified file is header file.
- isImageFile
```
public static boolean isImageFile(java.lang.String absolutePath)
```
  Return true if the file specified by absolutePath is image file of PARREC.
  
  Parameters:
  
  absolutePath - the file name including path information.
  
  Returns:
  
  true if the specified file is image file.
- createImage
```
public ModelImage createImage()
                       throws java.io.IOException,
                              java.lang.OutOfMemoryError
```
  DOCUMENT ME!
  
  Returns:
  
  DOCUMENT ME!
  
  Throws:
  
  java.io.IOException - DOCUMENT ME!
  
  java.lang.OutOfMemoryError - DOCUMENT ME!
- updateTransformMatrix
```
private void updateTransformMatrix(FileInfoPARREC fileInfo,
                                   ModelImage image)
```
- ConvertToMIPAVConvention
```
public static TransMatrix ConvertToMIPAVConvention(TransMatrix mat)
```
  Converts translation matrix to mipav specific format
- makeTranslationMatrix
```
public static TransMatrix makeTranslationMatrix(double[] translations)
```
  Makes rotation matrix based on image off-centres that were stored in header and converted to orientation-specific values.
- makeRotationMatrix
```
public static TransMatrix makeRotationMatrix(int[] size,
                                             double[] rotations)
```
  Makes rotation matrix based on image angulations that were stored in header and converted to orientation-specific values.
- getFileInfo
```
public FileInfoPARREC getFileInfo()
```
  Returns the FileInfoAnalyze read from the file.
  
  Returns:
  
  File info read from file, or null if it has not been read.
- getHeaderFile
```
public java.lang.String getHeaderFile()
```
  Returns:
  
  DOCUMENT ME!
  - getImageFiles
```
public java.lang.String[] getImageFiles()
```
    Returns the image file list.
    
    Returns:
    
    the image file list.
  - readHeader
```
public boolean readHeader(java.lang.String imageFileName,
                          java.lang.String fileDir)
                   throws java.io.IOException
```
    Reads the analyze header and stores the information in fileInfo.
    
    Parameters:
    
    imageFileName - File name of image.
    
    fileDir - Directory.
    
    Returns:
    
    Flag to confirm a successful read.
    
    Throws:
    
    java.io.IOException - if there is an error reading the header
    
    See Also:
    
    FileInfoAnalyze
  - readImage
```
public ModelImage readImage(boolean one)
                     throws java.io.IOException,
                            java.lang.OutOfMemoryError
```
    Reads an PAR/REC image file by reading the header then making a FileRaw to read the image for all filenames in the file list. Only the one file directory (currently) supported.
    
    Parameters:
    
    one - flag indicating one image of a 3D dataset should be read in.
    
    Returns:
    
    The image.
    
    Throws:
    
    java.io.IOException - if there is an error reading the file
    
    java.lang.OutOfMemoryError
    
    See Also:
    
    FileRaw
  - readImage
```
public void readImage(float[] buffer)
               throws java.io.IOException,
                      java.lang.OutOfMemoryError
```
    Reads in a PAR/REC image (first the header file, then the raw file)
    
    Parameters:
    
    buffer - Image buffer to store image data into.
    
    Throws:
    
    java.io.IOException - if there is an error reading the file
    
    java.lang.OutOfMemoryError
    
    See Also:
    
    FileRaw
  - writeImage
```
public void writeImage(ModelImage image,
                       FileWriteOptions options)
                throws java.io.IOException
```
    Writes a PAR/REC format image and header.
    
    Parameters:
    
    image - Image model of data to write.
    
    Throws:
    
    java.io.IOException - if there is an error writing the file
    
    See Also:
    
    FileInfoAnalyze, FileRaw
  - getOffset
```
private int getOffset(FileInfoPARREC fileInfo)
```
    Helper method to calculate the offset for getting only the middle analyze image slice from the 3D file.
    
    Parameters:
    
    fileInfo - File info.
    
    Returns:
    
    offset
  - updateStartLocations
```
private void updateStartLocations(FileInfoBase[] fileInfo)
```
    Updates the start locations. Each image has a fileinfo where the start locations are stored. Note that the start location for the Z (3rd) dimension change with the change is the slice. The origin is in the upper left corner and we are using the right hand rule. + x -> left to right; + y -> top to bottom and + z -> into screen.
    
    Parameters:
    
    fileInfo - DOCUMENT ME!
  - updateUnitsOfMeasure
```
private void updateUnitsOfMeasure(FileInfoPARREC fileInfo,
                                  ModelImage image)
```
    Updates the units of Measure in the file info based on the voxUnits from an Analyze Header.
    
    Parameters:
    
    fileInfo - -- an Analyze file Info that has already been read
    
    image - -- a ModelImage that the fileInfo needs to be attached to
  - getCompleteFileNameListDefault
```
public java.lang.String[] getCompleteFileNameListDefault(java.lang.String absolutePath)
```
    Gets the header and image file names given a header or image file name
    
    Parameters:
    
    absolutePath - header or image filename
    
    Returns:
    
    array [0] headerfilename [1] imagefilename
  - writeHeader
```
public void writeHeader(ModelImage writeImage,
                        java.lang.String headerFileName,
                        int beginSlice,
                        int endSlice,
                        int beginTime,
                        int endTime,
                        boolean rescale)
                 throws java.io.IOException
```
    Parameters:
    
    writeImage -
    
    headerFileName -
    
    beginSlice -
    
    endSlice -
    
    beginTime -
    
    endTime -
    
    rescale -
    
    Throws:
    
    java.io.IOException
  - buildParVolMap
```
private java.util.HashMap<java.lang.String,java.lang.String> buildParVolMap()
```
  - buildParSliceMap
```
private java.util.HashMap<java.lang.String,java.lang.Integer> buildParSliceMap()
```

Class FilePARREC

Field Summary

Fields inherited from class gov.nih.mipav.model.file.FileBase

Constructor Summary

Method Summary

Methods inherited from class gov.nih.mipav.model.file.FileBase

Methods inherited from class java.lang.Object

Field Detail

hdrEXTENSIONS

imgEXTENSIONS

fileDir

fileInfo

fileName

image

dtiparams

vox_offset

fileInfoArray

outInfo

VolMap

SliceMap

VolParameters

SliceParameters

Slices

version

patientName

examName

protocolName

patientPosition

foldover

sliceOrientPos

bValuePos

gradPos

echoNumberPos

dynamicScanNumberPos

cardiacPhaseNumberPos

imageTypeMRPos

scanningSequencePos

scanPercentagePos

windowCenterPos

windowWidthPos

imageAngulationPos

imageOffcentrePos

fmriStatusIndicationPos

imageTypeEDESPos

echoTimePos

dynamicScanBeginTimePos

triggerTimePos

numberOfAveragesPos

flipAnglePos

cardiacFrequencyPos

minimumRRIntervalPos

maximumRRIntervalPos

turboFactorPos

inversionDelayPos

diffusionBValueNumberPos

gradientOrientationNumberPos

contrastTypePos

diffusionAnisotropyTypePos

labelTypePos

contrastBolusAgentPos

contrastBolusRoutePos

contrastBolusVolumePos

contrastBolusStartTimePos

contrastBolusTotalDosePos

contrastBolusIngredientPos

contrastBolusIngredientConcentrationPos

sliceOrientIndex

bValueIndex

gradIndex

echoNumberIndex

dynamicScanNumberIndex

cardiacPhaseNumberIndex

imageTypeMRIndex

scanningSequenceIndex

scanPercentageIndex

windowCenterIndex

windowWidthIndex

imageAngulationIndex

imageOffcentreIndex

fmriStatusIndicationIndex